Double-emulsion droplet digital CRISPR/Cas12a for amplification-free, absolute quantification of nucleic acids at attomole levels

The quantification of nucleic acids is of prominent importance for biology and medicine sciences. Droplet digital polymerase chain reaction (ddPCR) provides an absolute measure of target nucleic acid molecules with unrivalled sensitivity and accuracy, but suffers from limitations inherent to PCR amplification, droplet partition, and signal detection. Here, we present an ultrasensitive, rapid, and high-throughput technique for the absolute quantification of nucleic acids without the need for amplification, by combining the double-emulsion (DE) droplet digital platform with CRISPR/Cas12a system (d³CRISPR). We demonstrate the developed approach by accurately quantifying various DNA molecules, such as target human papillomavirus (HPV) 18, HPV16, and E. coli DNA, at concentrations down to attomole levels. This represents an over 1,000-fold improvement in the limit of detection (LOD) compared to existing bulk analysis amplification-free Cas12a assays. Given the versatility and generality of the CRISPR system, we believe that this approach has great potential in the detection and measurements of diverse nucleic acid molecules for many biomedical, clinical, and environmental applications.